Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

Density functional study of hydrogen bond formation between methanol and organic molecules containing Cl, F, NH2, OH, and COOH functional groups

Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides < fluorides < alcohols < amines, while the contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.     

A Schiff-base porphyrin complex with double intramolecular hydrogen bonds

We have designed a porphyrin with a Schiff-base substituent as a model to study intramolecular hydrogen-bonding. The corresponding complex [Zn(SATPP)(CH₃OH)] has been synthesized and characterized by X-ray crystallography, ¹H NMR, and UV-Vis spectroscopy. The structure shows that there are three phenyl groups and one salicylideneaminophenyl group at the meso positions of the porphyrin, and the phenol oxygen is involved in double hydrogen bonds, one within the salicylideneaminophenyl and the other between coordinated methanol and phenol oxygen. ¹H NMR spectra suggest that the binding of methanol to zinc is an equilibrium process in solution and the equilibrium constant has been determined by UV-Vis measurements. The intramolecular hydrogen bond stabilizes the structure, and the binding affinity increases 10 times over the corresponding TPP (TPP, dianion of meso-5,10,15,20-tetraphenylporphyrin).     

Contribution of the intramolecular hydrogen bond to the shift of the pKa value and the oxidation potential of phenols and phenolate anions

Intramolecularly OHO[double bond, length as m-dash]C hydrogen bonded phenols, 2-HO-C6H2-3,5-(t-Bu)2-CONH-t-Bu (1-OH), 2-HO-C6H2-5-t-Bu-1,3-(CONH-t-Bu)2 (2-OH) and 2-HO-C6H2-3,5-(t-Bu)2-NHCO-t-Bu (4-OH), were synthesized and their phenolate anions were prepared as tetraethylammonium salts (-1O-(NEt4+), 2-O-(NEt4+) and 4-O-(NEt4+)) with intramolecular NHO(oxyanion) hydrogen bonds. 4-HO-C(6)H(2)-3,5-t-Bu(2)-CONH-t-Bu (3-OH) and its phenolate anion, 3-O-(NEt4+), were synthesized as non-hydrogen bonded references. The presence of intramolecular hydrogen bonds was established through the crystallographic analysis and/or (1)H NMR spectroscopic results. Intramolecular NHO(phenol) hydrogen bonds shift the pK(a) of the phenol to a more acidic value. The results of cyclic voltammetry show that the intramolecular OH...O=C hydrogen bond negatively shifts the oxidation potential of the phenol. In contrast, the intramolecular NHO(oxyanion) hydrogen bond positively shifts the oxidation potential of the phenolate anion, preventing oxidation. These contributions of the hydrogen bond to the pKa value and the oxidation potentials probably play an important role in the formation of a tyrosyl radical in photosystem II.     

Computational study on the molecular conformations of phenolic compounds

The study of the conformation of eight phenolic compounds (i.e. phenol, guaiacol, syringol, pyrocatechol, o-, m-, p-cresol and vanillin) was carried out using B3LYP (Becke, 3-parameter, Lee-Yan-Parr) method and cc-pVTZ (correlation consistent polarized polarisation Valence triple zêta) basis set. Potential energy surfaces were plotted in order to identify the minimum energy structures and the transition states. For the first time, structures of vanillin and syringol were completely determined. Moreover, our work also confirms that the most stable conformations of m-cresol and p-cresol are obtained when the methyl group presents a hydrogen atom at the perpendicular of the benzene ring. The possibility of intramolecular hydrogen bonding was also investigated. Guaiacol, pyrocatechol, syringol and vanillin present a structure stabilized by the presence of a moderate hydrogen bond. Finally, potential energy barriers and rotational potential functions were calculated. The comparison of the rotational potential parameters for each molecule highlights the presence of similarities specific to each substituent and their neighbours.     

Proton-coupled electron transfer versus hydrogen atom transfer in benzyl/toluene,methoxyl/methanol,and phenoxyl/phenol self-exchange reactions

Degenerate hydrogen atom exchange reactions have been studied using calculations, based on density functional theory (DFT), for (i) benzyl radical plus toluene, (ii) phenoxyl radical plus phenol, and (iii) methoxyl radical plus methanol. The first and third reactions occur via hydrogen atom transfer (HAT) mechanisms. The transition structure (TS) for benzyl/toluene hydrogen exchange has C(2)(h)() symmetry and corresponds to the approach of the 2p-pi orbital on the benzylic carbon of the radical to a benzylic hydrogen of toluene. In this TS, and in the similar C(2) TS for methoxyl/methanol hydrogen exchange, the SOMO has significant density in atomic orbitals that lie along the C-H vectors in the former reaction and nearly along the O-H vectors in the latter. In contrast, the SOMO at the phenoxyl/phenol TS is a pi symmetry orbital within each of the C(6)H(5)O units, involving 2p atomic orbitals on the oxygen atoms that are essentially orthogonal to the O.H.O vector. The transferring hydrogen in this reaction is a proton that is part of a typical hydrogen bond, involving a sigma lone pair on the oxygen of the phenoxyl radical and the O-H bond of phenol. Because the proton is transferred between oxygen sigma orbitals, and the electron is transferred between oxygen pi orbitals, this reaction should be described as a proton-coupled electron transfer (PCET). The PCET mechanism requires the formation of a hydrogen bond, and so is not available for benzyl/toluene exchange. The preference for phenoxyl/phenol to occur by PCET while methoxyl/methanol exchange occurs by HAT is traced to the greater pi donating ability of phenyl over methyl. This results in greater electron density on the oxygens in the PCET transition structure for phenoxyl/phenol, as compared to the PCET hilltop for methoxyl/methanol, and the greater electron density on the oxygens selectively stabilizes the phenoxyl/phenol TS by providing a larger binding energy of the transferring proton.     

Study of the interaction in clusters formed by phenol and CH3X (X=CN,F,Cl) molecules

The characteristics of the interaction between phenol and acetonitrile, methyl fluoride and methyl chloride were studied. The most stable structures for clusters containing one or two CH3X molecules and one phenol moiety were located by means of ab initio and density functional theory calculations. Phenol-acetonitrile dimer presents two almost equally stable structures; one of them is a typical linearly hydrogen bonded minimum, whereas in the other one, a C-H...pi contact is established accompanied by a distorted O-H...N hydrogen bond. Although the latter minimum presents the larger interaction energy, deformation effects favor the formation of the linear hydrogen bonded one. In complexes with methyl fluoride and methyl chloride, this arrangement is the most stable structure and no linear hydrogen bonded structures were located. Our best estimates for the interaction energies amount to -27.8, -21.6, and -19.7 kJ/mol for clusters of phenol with acetonitrile, methyl fluoride, and methyl chloride, respectively. The main contribution to the stabilization of these clusters is of electrostatic nature, although in structures where a C-H...pi contact is present, the dispersion contribution is also significant. In clusters formed by phenol and two CH3X units, the most stable arrangement corresponds to a head to tail disposal with O-H...X, C-H...X, and C-H...pi contacts forming a cycle. Only for this type of arrangement, three body effects are non-negligible even though they constitute a minor effect. The results also indicate that interactions with methyl fluoride and methyl chloride are of similar intensity, although weaker than with acetonitrile. Significant frequency shifts are predicted for the O-H stretching, which increase when increasing the number of CH3X molecules.     

Theoretical study of temperature and solvent dependence of the free-energy surface of the intramolecular electron-transfer based on the RISM-SCF theory: application to the 1,3-dinitrobenzene radical anion in acetonitrile and methanol

The free-energy surfaces along the intramolecular electron-transfer reaction path of the 1,3-dinitrobenzene radical anion in acetonitrile and methanol are investigated with the reference interaction site model self-consistent field theory. Although acetonitrile and methanol have similar values of the dielectric constant, the free-energy profiles are quite different. In the methanol solution, the charge is strongly localized on one of the nitrile substituents due to a strong hydrogen bond between 1,3-dinitrobenzene and the solvent, while the polarization is not so large in the case of acetonitrile. The temperature dependence of the reorganization energy, the coupling strength, and the activation barrier is evaluated in both acetonitrile and methanol. The reorganization energy and the activation barrier decrease with increasing temperature for both cases. The electronic coupling strength also shows a similar tendency in the temperature dependence; it increases with increasing temperature in both solvents but with different rates. The behavior is explained in terms of the strong polarization induced by the hydrogen bond between the solute and solvent in the methanol solution.     

Vibrational spectroscopic properties of hydrogen bonded acetonitrile studied by DFT

Vibrational properties (band position, Infrared and Raman intensities) of the acetonitrile C[triple bond]N stretching mode were studied in 27 gas-phase medium intensity (length range: = 1.71-2.05 angstroms; -deltaE range = 13-48 kJ/mol) hydrogen-bonded 1:1 complexes of CH3CN with organic and inorganic acids using density functional theory (DFT) calculations [B3LYP-6-31++G(2d,2p)]. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in the OH stretching band of the acids were also considered. Experimentally observed blue-shifts of the C[triple bond]N stretching band promoted by the hydrogen bonding, which shortens the triple bond length, are very well reproduced and quantitatively depend on the hydrogen bond length. Both predicted enhancement of the infrared and Raman nu(C[triple bond]N) band intensities are in good agreement with the experimental results. Infrared band intensity increase is a direct function of the hydrogen bond energy. However, the predicted increase in the Raman band intensity increase is a more complex function, depending simultaneously on the characteristics of both the hydrogen bond (C[triple bond]N bond length) and the H-donating acid polarizability. Accounting for these two parameters, the calculated nu(C[triple bond]N) Raman intensities of the complexes are explained with a mean error of +/- 2.4%.     

Effects of hydrogen bond and solvent polarity on the C=O stretching of bis(2-thienyl)ketone in solution

The optimized structural parameters, the absorption and the resonance Raman spectra have been investigated for the bis(2-thienyl)ketone in gas phase, in cyclohexane, methanol, and acetonitrile solvents by means of time dependent density functional theory calculations, the solvent electronic polarization effect on the solvation shift is examined and in well accordance with the calculation. The effect of increasing the polarity of the solvent is well represented by the polarizable continuum model, both for the absorption spectra and resonance Raman intensities. The Raman spectra of the C=O stretching mode, which is sensitive to the intermolecular interaction for bis(2-thienyl)ketone dissolved in solvents, were systematically studied. It was found that the hydrogen bond effect plays an important role in reducing the carbonyl stretching wavenumbers. The results of Raman shifts were interpreted through the dilution effect, solvation effects, and hydrogen bond-forming effects. Furthermore, the excitation profiles of several important Raman bands of bis(2-thienyl)ketone molecule in different solvents have been critically analyzed. The solvent effects on structural and symmetry properties of the molecule in S2 electronic state as well as the short-time photo relaxation dynamics have been discussed.     

Contribution of intramolecular C=O...H-N hydrogen bonding to the solvent-induced reentrant phase separation of poly(N-isopropylacrylamide)

Changes in the local environment around amide groups of poly(N-isopropylacrylamide) (PNiPA) during a solvent-induced reentrant phase separation have been investigated by infrared spectroscopy combined with quantum chemical calculations. The addition of methanol or tetrahydrofuran as a cosolvent to an aqueous solution of PNiPA causes spectral changes in the amide I regions. By preparing a dimer model compound for PNiPA, we can establish the assignment of the amide I bands for the polymer in solutions. Hydrogen-deuterium exchange experiments of the amide protons of PNiPA and its dimer models have revealed that the amide groups of PNiPA form an intramolecular C=O...H-N hydrogen bond even in a good solvent. The result has suggested that the change in the amide I envelope of PNiPA observed during the solvent-induced phase transition reflects the modification of the intramolecular C=O...H-N hydrogen bond of PNiPA as well as the variation in solvation state of the amide groups. On the basis of the assignment, we have discussed contributions of the intramolecular C=O...H-N hydrogen bond to the phase behavior of PNiPA.     

Structures of transient species in the photochromic reaction of 1′,3′,3′-trimethylspiro[2H-1-benzopyran-2,2′-indoline]: Time-resolved resonance Raman study of isotopically substituted analogues

Time-resolved resonance Raman spectra of seven kinds of isotopically substituted analogues of 1′,3′,3′-trimethylspiro[2H-1-benzopyran-2,2′-indoline] in the photomerocyanine form have disclosed that only the vibrations of the cleaved benzopyran part are resonance enhanced significantly in cyclohexane and in acetonitrile solutions with 460-390 nm probe light. Dramatic changes in the resonance Raman spectra of the photomerocyanine on going from non-hydrogen-bond donor solvents to hydrogen-bond donor solvents can be interpreted as being due to changes in the relative contribution of ortho-quinoidal and zwitterionic forms in the resonance hybrid structure of the photomerocyanine: in cyclohexane and in acetonitrile the contribution of the ortho-quinoidal form is substantial, while in methanol the zwitterionic form is stabilized by hydrogen bonding with the solvent and the photomerocyanine takes an almost zwitterionic structure.     

Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol

The time-dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen-bonded intramolecular charge-transfer (ICT) excited state of 4-dimethylaminobenzonitrile (DMABN) in methanol (MeOH) solvent. We demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O formed between DMABN and MeOH can induce the C[triple bond]N stretching mode shift to the blue in both the ground state and the twisted intramolecular charge-transfer (TICT) state of DMABN. Therefore, the two components at 2091 and 2109 cm(-1) observed in the time-resolved infrared (TRIR) absorption spectra of DMABN in MeOH solvent were reassigned in this work. The hydrogen-bonded TICT state should correspond to the blue-side component at 2109 cm(-1), whereas not the red-side component at 2091 cm(-1) designated in the previous study. It was also demonstrated that the intermolecular hydrogen bond C[triple bond]N...H-O is significantly strengthened in the TICT state. The intermolecular hydrogen bond strengthening in the TICT state can facilitate the deactivation of the excited state via internal conversion (IC), and thus account for the fluorescence quenching of DMABN in protic solvents. Furthermore, the dynamic equilibrium of these electronically excited states is explained by the hydrogen bond strengthening in the TICT state.     

5-巯基-1, 3, 4-噻二唑-2-硫酮微溶剂团簇的光谱和理论计算研究

微溶剂作用(即溶剂化过程)广泛存在于所有物理、 化学和生命过程中. 在液相化学反应体系中, 几乎是一切化学反应的基础. 通过傅里叶变换拉曼光谱(FT-Raman)并结合密度泛函理论(DFT), 表征了固态5-巯基- 1, 3, 4-噻二唑-2-硫酮(MTT)的结构, 并进一步确认了MTT在乙腈、 甲醇和水中微溶剂团簇的大小和氢键位点. 通过探究MTT在不同溶剂及pH条件下的紫外-可见吸收光谱(UV-Vis), 结合含时密度泛函理论(TD-DFT)计算, 揭示了溶剂和pH对MTT电子跃迁带的影响, 进一步解释了其光谱位移. 结合能量计算可以得出, MTT分别与1个乙腈、 2个甲醇和2个水分子形成MTT(CH₃CN), MTT(CH₃OH)₂ 和MTT(H₂O)₂团簇.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

DNA中糖苷键碱基侧二共价键的喇曼特性分析

分析小牛胸腺ＤＮＡ的纤维和水溶液两种状态样品的激光喇曼光谱发现，嘌呤碱基糖苷键两侧共价键Ｎ９Ｃ４与Ｎ９Ｃ８的喇曼特性表现不同，分析与它们相联的Ｎ３与Ｎ７原子在原子电荷、一级水合层中水桥的形成，以及核苷酸单位内氢键形成等方面的差异，可认为在ＤＮＡ水溶液中Ｎ９Ｃ４明显的减色性是因Ｎ３原子的特殊性质所造成。     

Intra- vs. intermolecular hydrogen bonding: dimers of alpha-hydroxyesters with methanol

Intermolecular hydrogen bonding competes with an intramolecular hydrogen bond when methanol binds to an alpha-hydroxyester. Disruption of the intramolecular OH...O=C contact in favour of a cooperative OH...OH...O=C sequence is evidenced by FTIR spectroscopy for the addition of methanol to the esters methyl glycolate, methyl lactate and methyl alpha-hydroxyisobutyrate in seeded supersonic jet expansions. Comparison of the OH stretching modes with quantum-chemical harmonic frequency calculations and 18O labelling of methanol unambiguously prove the insertion of methanol into the intramolecular hydrogen bond. This is in marked contrast to UV/IR hole burning studies of the homologous system methyl lactate: (+/-)-2-naphthyl-1-ethanol, where only addition complexes were found and the intramolecular hydrogen bond was conserved. This switch in hydrogen bond pattern from aliphatic to aromatic heterodimers is thought to reflect not only a kinetic propensity but also a thermodynamic preference for addition complexes when dispersion forces become more important in aromatic systems.     

Catalytic activity of iron-containing polymers in hydroxylation of benzene with hydrogen peroxide

Hydroxylation of benzene with hydrogen peroxide in aqueous acetonitrile at 50°C was studied. The KU-2-8 and KU-1 cation exchangers, and also specially synthesized cation exchangers and phenolformaldehyde resins derived from pyrocatechol and resorcinol, all modified with Fe(III) cations, were used as catalysts. The macrocomplex KU-2-8/Fe³⁺ showed the highest catalytic activity and ensured 32% yield of phenol in 15 min. The formation of phenol depends in a complex fashion on the initial concentration of hydrogen peroxide, content of Fe(III) ions in the polymer, and reaction time.     

The structure of liquid alcohols and the temperature dependence of vibrational bandwidth

To obtain the information about the structure peculiarities of liquid alcohols the temperature dependence of Raman profiles widths for these objects was studied. The results of these investigations have shown that in the region 150–340 K the widths of Raman bands in liquid methanol and ethanol are constant. From the data on the constancy of the number of hydrogen bonds per one molecule (in the same temperature range) the conclusion on the dynamic stability of the cluster structure of alcohols was made. The broadening of vibrational bands is determined by inhomogeneous broadening and by the dephasing of intramolecular vibrations due to the hydrogen bond dissociation.